Data Reduction Utilities in IDL and IRAF

Additional Michelle Data Reduction Tools/Utility Scripts

This page provides links to a number of IRAF or IDL tasks that are
useful utilities for either Michelle data reduction, or examining a
set of data. Some of the IRAF tasks are likely to be released with
the next revision of the Gemini IRAF package, whereas others are
private routines that are never going to be part of the Gemini/IRAF package.

The IDL utilities cannot be officially supported because they use IDL,
which is not freely available software, but are provided here for use by
Michelle PIs if they so wish.

Questions about these routines should be directed to Scott Fisher (IDL)
or Kevin Volk (IRAF). Note, however, that we do not guarantee that we will
be allowed to support these routines. You may be on your own with them.

The IRAF scripts were written by Kevin Volk, usually initially for
his own use, and so do not necessarily comply with the coding standards
that are enforced for the Gemini IRAF package. Some of the IRAF scripts
have a help page in the usual IRAF format, which can be displayed within
IRAF via the help command by specifying the path to the help file
and specifying the file_template flag. For example

cl> help /some/file/path/miclean.hlp file_template+

will show the help page for miclean.cl provided that the path
("/some/file/path/" above) is replaced by the proper path to where the file
is stored. Not all the scripts have help files at the moment.

The IRAF tasks can be defined at the IRAF prompt as in the following
example:

cl> task miclean = /some/file/path/miclearn.cl

where again one has to provide the proper path to the script file.

The IDL Defringing Widget

The IDL procedure mdefringe.pro is a widget for defringing
Michelle spectra working with the stacked data file. This procedure works
in IDL versions 6 and 7. It will probably not work in earlier versions of
IDL. The procedure can read in a Michelle stacked image and display a
two-dimensional fourier transform of the image. If one then masks out regions
of the fourier image with the cursor, these are blanked off. Once regions are
blanked off one can transform the fourier image back to the original domain
and see what effect the masking has had. Especially for Michelle medN2
spectroscopy this is able to get rid of a large part of the spectral fringes
in the data. It works better than the IRAF routine for defringing the
one-dimensional extracted spectra in the test cases we have been working with.

For low-resolution N-band spectra the defringing in IRAF is usually
quite sufficient and this tool is not needed for such data. For the medN1
Michelle spectral mode the results of using the IDL procedure appear to be
less satisfactory than is the case for the medN2 mode, but its still better
than what the IRAF defringing produces.

Noise Masking procedures

Once a stacked Michelle or T-ReCS image has been read into IDL, the
following two procedures can be used to remove vertical or horizontal
pattern noise. These are stand-alone IDL procedures, originally written
by Jim deBuizer (here is a link to
his professional web page
where there is a link to his IDL tools for T-ReCS image reduction for anyone
who may be interested).

Additional IRAF Utility Scripts

Links are provided below to the scripts and the associated help files
where these exist. A short description of each routine is provided.

miclean.cl

This is a script to remove certain types of noise from stacked Michelle
(or T-ReCS) images. It can in princple be used on raw data as well but
this is not recommended. The task generally is able to remove the channel
to channel offsets, vertical band noise, and horizontal band noise in Michelle
images.

mipql.cl

This script produces rough polarimetry maps (Stokes parameters and
the polarization vector quantities) from a stacked polarimetry
image produced by the mipstack routine. While it is not a substitute
for reduction using a polarimetry package, it does produce a good first look
at Michelle polarimetry data.

nodstack.cl

In some cases one may wish to stack the "A" and "B" nods separately.
This script carries out this operation. Note that telescope radiative
offset and sky residuals will be present in the stacked images. Nonetheless
in some instances it is useful to examine the two nod positions separately
if there is something unusual seen in the straight stack of the nod images.

minods.cl

The minods.cl script splits off the individual nod images from
a regular T-ReCS or Michelle raw data file or prepared data file and writes
these out to disk as individual simple FITS files. For polarimtery files it
is better to use mipsplit.cl for this type of purpose.

Again there is no help file for this script as it is reasonably simple in
concept.

mipsplit.cl

displayset.cl

The purpose of this task is to sequentially display a series of Michelle
stacked images, with the option of using imexam on each one. It is
useful if one downloads a large set of files from a Michelle program and
wishes to look at the various files to see what is what. Note that if one
has a set of raw data files these would have to be run through the
mireduce script as a group first before using this script.

mishownods.cl

Here is another data examination script. This one is intended to look
through the individual nods in a Michelle or T-ReCS raw data file (or a
"prepared" file) by displaying the nods in groups in the DS9 or XIMTOOL
window, with the option of going into imexam to look at each set of
NOD images. As with some of the other utilities here, this is most useful if
something unusual appears to be present in a stacked Michelle or T-ReCS image.
In normal IRAF one may be limited to 4 images displayed at once, but in PyRAF
I think one can go up to 16 images at once.